Guidelines for the use of antiretroviral agents consider that viral load values may differ using the branched DNA (bDNA) and polymerase chain reaction (PCR) methods. Whereas the most commonly used PCR assay (Amplicor v1.5, Roche) targets HIV gag sequences, the bDNA (Quantiplex v3.0, Bayer) is based on the recognition of HIV pol sequences. The possibility that accumulation of drug-resistance mutations at the reverse transcriptase and/or protease genes could influence viral load measurements using bDNA was examined in a case control study. Plasma samples collected from 46 HIV-infected individuals receiving antiretroviral therapy and carrying different number of drug resistance mutations were analyzed. The performance of both bDNA and PCR assays was found to be comparable irrespective of the presence or absence of drug resistance mutations.